How to draw circle or rectangle or arrow in blender video editor?
Here is what I do (or something similar, as I use this tactic to position more videos for people to click on), you can create a simple box with transparency around it (though make sure that the image format you save it as has support for alpha, png should work):

Get your image onto your sequencer (drag in the image, or Shift + A).



Select your image (Right click), and press Shift + A , then choose Effect Strip, and then Transform.



Select the Transform block/strip, then over on the right, choose
Alpha Over instead of Replace.



Change the position and scale settings on the right, in the Effect Strip